A Tangled Web
by Mewkey
Summary: Summary inside. Part two of 3 prequels to the Movie trilogy. Be sure to check out part three, An Unexpected Ending.
1. The Architect

Disclaimer: The Wachowski Brothers, Warner Brothers, Joel Silver, and any number of other people own the rights to The Matrix and any and all related characters/content. Not me.

Caveat: If anyone has read my Beetlejuice fan fiction they know I am the queen of super short chapters. I apologize for this, but such is the nature of my muse. She makes me break things up in a certain way and I must obey her.

Synopsis: If you haven't read my first Matrix fan fic, In The Beginning, you're going to want to read that before proceeding. This is part two of a series of prequels to the Matrix movies. It's been five years since Christopher Inizio, called "Abe" by his people, freed himself from The Matrix. Now he works to free other humans from the machines' energy collectors. But his life is far from simple, and his problems have just begun.

Special disclaimer for chapter 1: This story is once again entirely not my own. True, I've inserted my character and the events from my previous fiction into it, but the story remains entirely not mine. This chapter is my retelling of the story The Architect tells Neo in Matrix: Reloaded. I won't make any money off this story so please don't sue me. From a literary standpoint, this story had to be told.

I now present to you: A Tangled Web

* * *

A man with pure white hair, dressed in a white suit, sat silently watching hundreds of monitors showing every aspect of an event that troubled him greatly. He pinched the bridge of his nose, closing his eyes and sighing quietly. He never ceased to marvel at the extremes the human mind would go to simply to maintain their right to suffer.

He had created a simple and yet elegant program once. He had seen in the minds of countless humans their ultimate goal of salvation and Utopia and he had written a program to give them that. The program was flawless. The humans, however, were not.

Their minds absolutely refused to accept the program. Their tiny, insignificant, primitive human brains just simply could not believe perfection could exist on such a grand scale. So he had gone back to the drawing board.

He consulted the entirety of human history and wrote another program, still simple and elegant, that he thought would placate the humans. His new "Matrix" gave an experience identical to humanity at the end of the 20th century. This seemed to work for a time, but soon more and more human minds began to reject this program just as they had the first. Their minds, somehow aware that his program wasn't real, were screaming to be released. So he had created _her._

She was an intuitive program designed specifically to discover why so many humans simply refused to accept his program as their reality. She probed deeply into the human population, too deeply as he had just recently found out, and discovered a possible problem: choice. He had never allowed the force-grown clones to decide for themselves whether to be a part of the program or not. That lack of choice, lack of free will, created the struggle against the program. It wasn't as strong in some humans as it was in others, but ultimately it was a problem (an anomaly if you will) that could destroy his carefully laid out plans. So he set to work again, creating a program that inserted choice into the mix of processes.

This single variable, though, had lead to an unbalanced equation. He had thought he could contain that anomaly, could control the variable. The humans began to be offered, subconsciously and unknowingly, the choice to accept the program or to be set free from it. If they chose to remain a part of the Matrix then they were kept attached to it. If they chose freedom, they were quietly and secretly taken out of 01 (the machine city) to be dropped near the one remaining human settlement: Zion. The humans, completely oblivious, always took the "orphan" in. And so, a new balance was achieved.

There were always some minds that would ultimately reject the program. Alarmingly, he had come upon them more and more often in recent years. Until now, he had always been able to send his agents to collect the mind and clear it before anything unsettling had happened. For some reason, however, Christopher Inizio had been immune to the influence of his agents. And Christopher, aided by the intuitive program now calling itself the Oracle, had freed himself.

Now the problem was no longer one he could ignore. Escalating attempts culminating in a success meant one thing to him: he was no longer able to control the anomaly introduced by giving the humans choice. But he knew from previous experience he was also not able to control the humans when no choice was given.

The choice itself was also getting out of hand. The number of humans choosing not to be inserted into the Matrix was growing at an exponential rate. He felt control slipping through his fingers.

Very well. He began to write a new bit of code…a myth for the humans. It would be a messianic story, to placate their religious tendencies. This code would be fed to them if they chose to be separated from the Matrix. Every generation or so, an extra bit of code would be fed to one human who would then be termed "The One." This human would be allowed out of the Matrix, be allowed to bend and shape the Matrix to his will. Then, he would be brought here. The true nature of the Matrix would be revealed and "The One" would reset the program. Then they would begin again. Meanwhile, he would send machines to dispatch the human city Zion and "The One" would be allowed to take a contingent of humans from the Matrix to rebuild the city. In this manner, the anomaly would be kept at bay, controlled as he had not been able to control it before.

He smiled slightly as he watched Christopher disappear for the nth time from his monitors. _They will call me The Architect_, he thought to himself, _and as such I suppose I am._


	2. The Oracle

Disclaimer: The Wachowski Brothers, Warner Brothers, Joel Silver, and any number of other people own the rights to The Matrix and any and all related characters/content. Not me.

Caveat: If anyone has read my Beetlejuice fan fiction they know I am the queen of super short chapters. I apologize for this, but such is the nature of my muse. She makes me break things up in a certain way and I must obey her.

* * *

Seraph helped the Oracle sit at her kitchen table. She was having trouble adjusting to this most recent change. Smith and the other agents had nearly annihilated her core programming, but Seraph had stopped them in the nick of time. Now, he was just finishing the upload of her old program files. Or, to put a human face on it, Seraph was just tending to her last wound. She'd be back to herself in no time.

The Oracle leaned back with her eyes closed for a moment, breathing evenly. Seraph stood silently at her side. Her eyes opened slowly and she gazed across the room at her toaster, regarding her new face in its reflection with curiosity.

"You know, Seraph…every time this happens, a part of me kind of hopes they'll bring me back as a buxom blonde. But, I guess that image doesn't really fit with the mystique, does it?"

The Oracle gave a short, bitter laugh. Seraph merely regarded her with the same impassive face he always wore.

"How do you feel?" he asked her.

"Old," she replied. "Old and feisty. I like this new face. There's alotta livin in this face. So," she said, lighting a cigarette slowly, "any news from Christopher? Did he make it?"

Seraph allowed himself a small smile.

"You already know the answer to that, Oracle."

"Yes I do. Can't get anything past you, can I?"

She took a drag on her cigarette and looked up at Seraph.

"Five years is a long time, Seraph."

Seraph nodded once in acknowledgement.

"Well…let's get started then."

Seraph nodded again as he pulled his keyring from his pocket and headed for the door.


	3. Christopher and Miranda

Disclaimer: The Wachowski Brothers, Warner Brothers, Joel Silver, and any number of other people own the rights to The Matrix and any and all related characters/content. Not me.

* * *

Christopher lay awake for a long time, staring at Miranda. It had been a long day, and he still couldn't quite believe it was true. They were married now, bound to one another, their binding witnessed by friends and family.

Miranda gave a contented sigh in her sleep and moved closer to Christopher. He enfolded her in his arms, gently so that he didn't wake her, and kissed her eye lids softly. He laid his head back on his pillow and stared at the rocky walls of their quarters, remembering what had brought him to this moment…

--

At first, it had been hard to convince Christopher that he was no longer part of the Matrix.

Miranda and Andy had worked for hours to convince him. When his mind finally accepted that it was no longer attached to the mainframe, the relief that flooded his body was so intense he lost consciousness again. It was good this time though, a restful unconsciousness that would help him to repair his body. Those first few frenzied moments of intense activity when he was escaping the pod had injured his atrophied muscles in many ways. Andy thought it would take months for Christopher to recover.

Miranda had left Christopher in Andy's care. Through electro-stimulation and acupuncture Andy slowly nursed his ward to health. Here and there, Miranda would visit Christopher and talk with him, explaining the world to him while he listened in rapt silence. After a time, Christopher's stomach accepted the thin, nutrient-laden gruel the ship's crew lived on. His strength increased immeasurably after his first meal.

After a week Miranda's ship, the Osiris, had returned to Zion and Christopher was transferred to the main medical facility. There he was able to complete his healing, and a mere three weeks after he had been found by the Osiris Christopher was completely healed.

Christopher and Miranda saw a lot of one another after that. She helped him to understand how this dark world functioned. She introduced him to what passed for a ruling council and to the leaders of what functioned as a military.

"I have to admit," she told him one day, "we're pretty disorganized. You'd think after a century we'd be a little better equipped. But there were so few of us when we first came here, and we're to this day constantly finding more and more human orphans along the frontier. Every orphan has to be trained and taught by one of us, which means every orphan means one less person building ships or writing laws. It's necessary, though. Above all else, we believe in the sanctity of human life and we would never leave one behind."

The most surprising thing was Zion's reaction to Christopher. Beginning with the council and moving through many of the military leaders, a sense of awe began to radiate from people when he walked past them. Even before he saw the first real evidence of it, Christopher felt that they were beginning to regard him as a God. No one, in human or machine history, had ever actually succeeded in freeing themselves from the Matrix. It made Christopher uncomfortable and Miranda could tell. She was sympathetic but she began to call Christopher her "reluctant messiah," using humor to try and take the edge off for him.

Christopher had spent his time after his recovery trying to make a place for himself in Zion. He helped Miranda as much as possible, though he wasn't what you would call a military man. He mostly worked on the shipboard computers. Christopher kept the brain of the ship running while Marco (first mate and mechanic) kept the body running.

After a couple years, Christopher confessed his love to Miranda. She had been caught off guard, but it didn't take long for her to confess she loved him too. To hear Andy tell the story, their love (at least from Christopher's point of view) had been inevitable.

"Dude," Andy said to Marco on the night they found out Christopher had proposed to Miranda, "you should have seen the way this weak ass fool looked at her from the operating table when we first picked him up. He was besotted. He followed her like a damn puppy dog whining for a bone!"

Andy and Marco had dissolved into shouts of laughter after this, Christopher and Miranda both throwing playful punches at them.

Christopher had hesitated to draw Miranda into his world. True, she was already a part of it (the most important part), but he didn't know how she would feel about being the wife of the "reluctant messiah." Already, the people of Zion whispered devotions to him and brought him offerings. Already, they called him "Abe" as the Oracle had prophesized (their logic was "Christopher" was the name the Matrix gave him, but "Abe The Mudoken" was the name he gave himself. He often wondered if they knew how idiotic the name sounded outside of cyberspace). He knew there was no way to stop Zion from seeing him the way they wanted…needed…to see him. That didn't mean he had to be ok with it…and it didn't mean he had to drag her into it.

Surprisingly…and thankfully…she hadn't minded one bit. Miranda dealt with the throngs who came to see Christopher every day with a smile and never complained when the time came to share her man with her people.

"Just reserve a little time for me every day," she whispered to him one night, "and promise our lives won't change just because we're married. Promise we'll always be ourselves."

"I promise," he replied, leaning in to kiss her softly.

Their wedding had been a quiet affair. Christopher didn't want to turn Miranda into something to be gawked at, if he could help it, so the ceremony was held on the Osiris. Miranda's crew was there, along with the council and the captains from the other four ships in the fleet. Christopher and Miranda had quietly pledged themselves to one another, shared a chaste kiss in front of the assembled company, and that was that. Now Zion's reluctant messiah had a queen by his side.

--

Christopher hadn't realized he'd fallen asleep, his memories slipping effortlessly into dreams, until he felt Miranda leave their bed. His eyes snapped open and he watched her dressing for a moment before grabbing her wrist and tugging her back toward the bed.

"Nope," he said, his voice clogged with sleep, "you ain't going nowheres, little lady. You get right on back in this here bed."

Miranda giggled as she allowed herself to fall into the bed next to him, curling into a ball on her side and throwing an arm across his body.

"Sorry, partner," she giggled, "but I've got to git. The Osiris has patrol this morning."

Miranda felt his arms and legs wind themselves securely around her, making it impossible to move.

"Nope. No patrol for you, love. You're staying right here."

"Chris," she groaned, "come on, you know I've gotta go. It's only four hours. I'll be back before you know it."

"Nope." His grip tightened.

"I'm sorry I have to do this to you, Chris, but you leave me no choice."

Miranda began to tickle Christopher, giggling to herself. He jerked himself away from her, laughing loudly.

"Aw, come on Randa, that's not fair! You play dirty!"

Miranda sat on the edge of the bed, pulling on her leggings. She looked over her shoulder into Christopher's eyes, shaking slightly with silent laughter.

"You love it," she said when she had calmed the giggles. "Besides, you should probably get up anyway. You've got to get ready for your meeting with the council."

"That's not till next week. Hey," he said, coming up behind her and wrapping his arms around her shoulders, "don't go. We just got married, for Christ's sake. I need you today."

She hooked her hands onto his arms and leaned back against him for a moment, eyes closed. He was winning, she felt it. And was it so bad to let him win?

Miranda sighed as she grabbed her radio to contact the Osiris, intending to ask if there had been any com activity that morning. Activity meant the machines were plotting, which would give her an excuse for leaving Christopher today. If she was going to win this mini struggle for power, she'd need an excuse to extricate herself from her husband's warm embrace. Besides, Christopher had promised her their lives wouldn't change just because they were bound to each other. When was the last time he remembered her taking a day off for _any_ reason?

"Marco, you there?"

The radio crackled for a moment, and Andy's voice answered.

"Marco says he's not speaking to you today, boss."

"And why's that?!"

"Well, he figures if he doesn't talk to you then you don't have any excuse to go on patrol with us."

Miranda felt Christopher grin into her shoulder. His arms moved down her body, his hands gripping the hem of the tunic she had thrown on. _This is mutiny_, she thought.

"Chris got to you, did he?" she asked Andy, trying to smack away Christopher's hands. She was answered only by silence. "Andy? Respond, damn it!"

Christopher succeeded in pulling off Miranda's tunic with one hand as he took the radio out of her fist with the other. He rained kisses on the back of her neck as his hands began to explore her body.

"You have the best crew in all of Zion," Christopher whispered into her neck.

Miranda tried to sit and stew. Both her crew and her new husband knew she hated to be idle. Soon however, Christopher's insistent hands and urgent mouth made it difficult to think at all. She turned to face him, quickly slipping off her leggings and throwing her arms around him. Their lips met in a passionate embrace, the Osiris and her day's work entirely forgotten.


	4. Conversations

Disclaimer: The Wachowski Brothers, Warner Brothers, Joel Silver, and any number of other people own the rights to The Matrix and any and all related characters/content. Not me.

K this is filler. I needed to get from one point to another. I don't think this actually hangs together as its own chapter, but it doesn't quite work added to the previous chapter either. Sorry. I need an editor...

* * *

"She'll be out of commission for a while," Andy chuckled to himself. "Anything on the com channels, Marco?"

"Not a damn thing, same as every day. Why do we do this? If the machines haven't come for us now, I don't think they're gonna."

Marco flipped four switches and the four hover pads on the bottom of the ship hummed to life. He put his headset on as he eased the Osiris into the air.

"They want to be cautious," Andy replied. "Just because it's been ten years doesn't mean the machines aren't up to something. There's been a lot of com traffic during the night shifts…they're changing something but we…"

"Yeah yeah," Marco cut him off. "I know I know. We don't know what they're changing and we're afraid they're coming after us blah blah blah."

"Exactly. So let's get on out there and see if we can turn anything up!"

--

Several hours later, Christopher finally let Miranda out of bed long enough to get some food. She had radioed the Osiris for a report (more radio silence, punctuated by stifled laughs from her mutinous crew) and now sat thoughtfully munching her midday meal.

"I was thinking," she said to Christopher, "when you speak to the council next week, I don't think you should take me or the other captains with you."

Christopher, who had been washing his face, turned to her.

"Why is that, exactly?" he asked.

"Well, I don't think the captains will be as…sympathetic…as I am."

Christopher began to grumble and Miranda held up her hand.

"Just listen. I believe in what you want to do because I was the one who found you when you got out. I have seen the end product of the machines' batteries. And I haven't complained once when you used the Osiris to find places in the old maintenance tubes to get a good enough signal to hack into the Matrix. But Chris, not all of the captains will see things the same way I do. They're not all going to want to commit time and manpower to hunting down people in the Matrix to clandestinely free when they could be using that time and manpower to strengthen our defenses. And now, with all the com chatter at night, they're going to be that much more worried about protecting Zion over freeing people from the Matrix."

"Randa, listen. I know what their objections will be…"

"Chris, seriously. They still feel, on the whole, that once we've defeated the machines once and for all we'll be able to free everyone from the Matrix. That's all they're concerned with."

"But will we ever really have enough people to do it? Listen to me for a minute, Randa. Even if we waited another ten or fifteen years we still wouldn't have enough bodies to make an assault against the machine city. You've seen it, love. You've seen the human clone fields and the tens of millions of Sentinels in zero one. I believe the only chance we have is to begin 'clandestinely' freeing humans from the battery pods. We need more people like me, Randa…people who can fight them from the inside while you and the other captains fight them from the outside."

Christopher ran his hands over his head, feeling the short stubble of his hair. He kept it short as a reminder of where he came from.

"We need the people in the Matrix just as much as we need you and the other captains. If you don't want to go with me to meet with the council, that's fine. But I will need the other captains to be there. I mean, I'm not going to ask the council to give me ships to use when their captains aren't present to object!"

Miranda knew what he meant. He would never take the choice away from the captains. She knew his work was important, even vital, and she also knew just how much he needed more ships than the Osiris to be successful. But Christopher would never order another man to do something against his will. He hoped not only to win over the council next week, but also to win over the captains. Miranda sighed as she rose and crossed the room to where he stood. She pulled him into a warm embrace, holding him close.

"I know," she whispered. "I know, and I understand. We'll be there, all of us. Just remember who these men and women are, Chris. That's all I'm asking."

Christopher buried his face in her hair, holding her tightly.

"If it ends up that you're my only ally," he said, "then I'll make do with what I can get. I just hope the council sees things my way."

"So do I, Chris. So do I."

--

The week passed quickly and suddenly, Christopher found himself standing outside the council chamber trembling with nerves. Beside him, Miranda squeezed his hand.

"Ready?" she asked.

"As I'll ever be," he replied.

He took a deep breath and stepped into the chamber.


	5. Christopher’s Speech

Disclaimer: The Wachowski Brothers, Warner Brothers, Joel Silver, and any number of other people own the rights to The Matrix and any and all related characters/content. Not me.

* * *

"Thank you for seeing me today. I have asked that the captains join us because what I have to say concerns them just as much as it does the rest of Zion. I thank the council for its indulgence in this matter.

"As you are all aware, five years ago I was able to detach my mind from the machine mainframe program, called the Matrix. Though you've repeatedly questioned me as to how I accomplished this I have never been specific with that information. Until now.

"While connected to the mainframe, I used to suffer 'dreams' that were really my mind trying to wake me up to what reality really was. In my dreams, I saw the pods the machines keep humans in. I saw the vast energy collectors the pods were connected to. They terrified me.

"Within the Matrix, I received help from someone calling herself "The Oracle." I don't know if she was a sentient program or another human. She helped me to see the truth…to see that my dreams weren't really dreams at all, but reality trying to break through the haze the machines kept my mind in. It wasn't difficult to believe her story when she told me the history of humankind. My dreams had opened me up to all sorts of possibilities. She gave me the tools I needed to awaken my own mind and free myself from the Matrix.

"Over the past few months, with the help of my wife Miranda and her able crew, I have been systematically hacking into the Matrix mainframe in an effort to create a program that will warp the Matrix in a similar way to how the Oracle warped it to help me escape. The Oracle had created a scanning program that found my unique code signature and then disabled all controls both inside and outside the Matrix construct, thus allowing me to wake up and free myself from the pod. I have been able to create and test a similar program that has been successful. This program has been causing a lot of confusion in Zero One, and has been the cause of all the com chatter the other captains have heard at night. I know this might seem risky, but I have been able to keep both our ship and Zion herself safe by running programs similar to computer viruses while testing my trace program. The virus programs kept the machines busy enough that they were not able to track us down or link us to Zion. In fact, the machine mainframe thinks there's a rogue machine planting viruses as a prank.

"Using my program I am able not only to disable the internal and external controls preventing escape, but I am also able to force the mind to wake itself up. In this way, freeing a human from the Matrix will be accomplished much more quickly and easily than by using the method the Oracle used on me. With my program, we would not have to rely on the mind waking itself as mine did. We could simply choose a human, launch the program, and free the mind.

"Council members, I have now come to the crux of our meeting today. At this phase in my plans, I find myself in need of more resources than I've so far been able to use. Miranda has been generous enough to allow me to monopolize her ship and crew through long nights of testing, and now I must ask the same of each of the other four captains and ships. You see, my months of research and testing have gotten me to the point where I am certain I will be able to free another human from the Matrix. Indeed, I will be able to free many minds. But in order for this to be successful, I will need the help and support of every ship in our small fleet. Miranda and the crew of the Osiris will not be able to support this endeavor alone. All I am asking, for now, is for one of the three night patrol ships to be engaged in freeing humans from the Matrix. As we free more people, we will be able to build more ships and eventually we will be able to dedicate two or three ships solely to the freeing of all Matrix-bound humans.

"I can see the objections in your faces already. I know that the council and the captains are of the opinion that the humans in the energy collectors can safely be kept there until we are able to mount an attack against Zero One. I respectfully disagree. In the five years I have lived among you I have seen great strides forward toward that goal, but I don't believe it will be enough. Our numbers dwindle year by year, despite finding orphans along the frontier. I simply do not believe we will ever truly have the man power to mount such an impressive attack. The humans in the energy collectors need our help now. They cannot afford to wait the decades, or possibly centuries, it may take for us to be able to launch an attack that could end in the defeat of all mankind. If we begin to systematically remove humans from the energy collectors, we accomplish two feats that will help us dramatically in our fight to reclaim Earth. Firstly, we will add to our numbers faster than ever before. Those that we add will be vital assets in the coming war. Secondly, we will diminish Zero One's primary energy source, forcing the machines to begin to rely on alternative energies. This will weaken the machine forces while strengthening ours. I do not pretend that this alone will guarantee us victory over the machines, but it will vastly improve the odds that are so very much stacked against us right now.

"I do not know all the answers. I cannot give you a plan that will ensure humanity will survive. Hell, I can't even guarantee I'll be able to free as many humans as I believe I can. But for the sake of all humanity, I strongly feel that we need to try. We need to begin rescuing humanity from the machine batteries now. I thank you for listening to me."


	6. Reactions and Accusations

Disclaimer: The Wachowski Brothers, Warner Brothers, Joel Silver, and any number of other people own the rights to The Matrix and any and all related characters/content. Not me.

At this stage in my fic, I've decided to change the name of Miranda's ship from the Breaking Dawn to the Osiris. I figure I should use established cannon rather than make up my own ships or whatever lol. I've made changes to all the previous chapters to reflect this name change.

* * *

The council chamber erupted into shouts. All of the captains except Miranda, as well as all the council members except Kenton (the leader), began talking at once at the top of their voices. Miranda winced as she saw frustration flit briefly across Christopher's face.

Kenton regarded Christopher with an appraising stare. Christopher stood silently, arms crossed, staring at the ceiling while he waited for the noise to cease. Kenton looked at Christopher a moment longer and then raised his hand to quiet the chamber.

The captains and council members seemed hell bent on bringing down the walls with the noise they were making. Stephen of the Nebuchadnezzar was now pointing an accusatory finger at Christopher, screaming unintelligibly. Kenton stood slowly and took a deep breath.

"SILENCE!"

The council and captains fell silent so quickly the room seemed to ring for a moment. Kenton folded his hands and stood, beaming a radiant smile at the rest of the assembled. Christopher took his eyes from the ceiling and fixed them on Kenton. Miranda reached out impulsively to take Christopher's hand.

"There now. I think that will do for the shouting portion of the evening. If my fellow council members will join me at the table, I believe we can get back to business."

Stephen and Marlin (captain of the Gnosis) returned to their seats, accompanied by Leah of the Avatar and Samuel of the Logos. Reinette, Margot and Gregory were the first of the council members to sit, followed closely by the twins Sasha and Cassandra. Only Michael, second in leadership to Kenton and the youngest of the council, remained standing. He walked over to Christopher, staring him straight in the eye.

"Regardless of what may be said from this moment on, you have endangered the lives of all of Zion with your recklessness. Think on that."

Michael returned to his seat and was silent through the rest of the meeting, having spoken his mind. Kenton shook his head slightly at his colleague's temper and then focused on the seated captains.

"I first would like to hear from Zion's brave captains…"

"Oh, can we cut through the bullshit please?"

Marlin's voice rang out over the assemblage, cutting through Kenton's careful tones. Kenton regarded her as she rose to speak.

"Master Kenton, with all due respect, you really don't have to talk like an old Earth novel. Now Chris," Marlin turned to face Christopher, "you know I love you like a brother. But this kind of hair-brained shit I cannot support you in. We need our ships to make sure Zion stays safe. And if you're the one causing all the chatter on the com lines you're going to have to stop it. No matter how many computer thingies you shoot off to zero one, they're gonna figure it out eventually. Once they find you, they find all of us and poof! No more human race. Master Kenton, the Gnosis won't help Chris."

As Marlin sat back down, Leah stood to say her piece.

"For many months now, as this council knows only too well, I have been fighting Christopher's fight. I, too, feel that the time is ripe to begin freeing our kind from the energy collectors. Master Kenton, the Avatar stands ready to assist in any way we can."

Samuel was next. He put a steadying hand on Leah's shoulder for a moment before taking his place before the council table.

"I'm not one to make speeches. Master Kenton, the Logos also stands ready to assist."

Samuel smiled sheepishly at the other captains as he turned to resume his seat. The council chamber was silent for a moment as Kenton's gaze fell on Stephen. Stephen sat rigidly, arms crossed over his chest and a scowl fixed firmly upon his face.

"Stephen?" Kenton asked. "Would you care to share your views on the matter?"

Stephen stood silently, glaring at Christopher.

"I feel it is beneath me to even listen to this plan. Christopher may cost us hundreds of lives just to save a handful from the pods. It is suicide."

"Then may I assume you will not offer assistance?"

"Master Kenton," Stephen spat out, "the Nebuchadnezzar _respectfully_ declines to help this fool, Christopher."

With that, Stephen stalked out of the council chamber. Kenton sighed softly, closing his eyes for a moment.

"Miranda," Kenton said, "I will assume the Osiris will continue to aid Christopher. You needn't give a speech. Now, I should like to hear from the council members."

Sasha, Cassandra, and Margot all rose as one.

"We three are of the opinion," Margot said, "that Christopher's plan is sound. We approve the measure."

Sasha and Cassandra nodded their agreement, and all three women sat. Gregory stood next, his face troubled.

"Much of this seems staged to me. To be able to make such a profound decision so quickly suggests prior knowledge."

"I will admit," Christopher said, "I had spoken to several council members prior to this meeting, and Miranda spoke to the captains. I was never able to gain an audience with you, Kenton, or Reinette. I apologize for this."

Christopher bowed, and Gregory returned the bow.

"I believe, in this situation, I must go with my first instinct then. Christopher, the com traffic concerns me greatly. All you have done so far is test a single program while running several interference programs. This has caused so much com traffic at night that all our captains are constantly on edge. I fear if you continue, and perhaps succeed in freeing another human like yourself, it will push the machines into some sort of assault. This must be prevented at all costs. I'm sorry, Christopher, but I must side against you. I do not approve the measure."

Reinette stood quickly.

"Gregory, you are too kind. I think Christopher wants Zion to fall. How much do we really know about him? He was pod born…a force-grown clone of a human being! He could be a machine agent!"

"Reinette," Kenton began, "calm yourself…"

"I will not! Kenton, you may coddle this…this _person_, but I certainly will not. Not only do I not approve the measure but I will personally see to it that you never set foot on another ship again, Christopher!"

"Enough! Reinette, you opinion has been noted," Kenton said, "But let me remind you that you have no individual authority to keep him from the Osiris."

"To allow him to remain a member of the crew of that ship is suicide for both the Osiris and Zion!"

"Sit down, Reinette!"

The venom in Gregory's voice shocked Reinette into silence. She threw a mutinous look at him before turning on her heel and marching out of the chamber. Gregory nodded respectfully at Kenton before sitting.

"Which brings us to me," Kenton said. "If it were up to me, and only me, I would side with Gregory. The risks are great and, in my opinion, outweigh the rewards."

Christopher's face fell. He opened his mouth to protest but Kenton held up his hand, forestalling Christopher's words.

"I'm not finished, Chris. Leaving myself out of it, the council seems to be evenly split. Tellingly, however, the majority of the captains seem to be in your corner, Chris. And I can't ignore that. So I suggest a compromise. I suggest the Osiris, Avatar, and Logos take the night patrols. Each night, Christopher can work with a different ship to further his plans. In this way, the captains who are…less than sympathetic to your cause…will be kept from becoming collaborators. As for the council members who object…well, the only trouble will be from Reinette I believe. I think myself and the rest of the council can at least help her to be civil. Are we all in agreement?"

Murmurs of assent ran through the assemblage.

"Then it is settled. A fortnight from tonite this rotation will commence. In the mean time, Chris, what do you say you knock off the nightly hackings so the machines will calm down for a while, hmm? Perhaps leaving them alone will make them drop their guard and prolong our safety. I'm sorry to doubt you, Chris, but I fear once you start your campaign the machines will find you faster than you can find minds to free."


	7. More Conversations

Disclaimer: The Wachowski Brothers, Warner Brothers, Joel Silver, and any number of other people own the rights to The Matrix and any and all related characters/content. Not me.

* * *

Miranda stayed behind in the council chamber at the request of Kenton, so Christopher stood alone in the hallway waiting for her. Further down the passage, he heard Reinette crying and Stephen trying to comfort her. He stood as quietly as possible, hoping Miranda would be beside him before he met Stephen and Reinette. Unfortunately, before he realized it, they were rounding the corner and nearly knocked him down.

Christopher stifled his urge to run away from the pair as they regarded him with icy glares. Reinette was the first to break the silence.

"So here he is, the abomination. Stephen, where are your manners? Don't you know you must prostrate yourself before the immortal God Christopher? Quick, now, before he loses his temper!"

To Christopher's intense embarrassment, Reinette threw herself down to the ground before him, pressing her alabaster face into the floor.

"Is this low enough, my lord, to please you? Would you like to step on my neck? Perhaps snap it so that I may be the first _human_ to be sacrificed?"

The way she accented the word "human" made it entirely too clear that she regarded Christopher as anything but.

"Stand up, Reinette," Stephen hissed through clenched teeth. "Don't debase yourself in front of _it_."

Christopher jumped at the word "it." No one had ever referred to him in that way before. He couldn't bring himself to look at the pair as Reinette pushed herself up. Stephen took Reinette's arm and lead her away down the passage.

"Mark my words, boy," Stephen shouted over his shoulder. "Your end is coming."

--

"Miranda, you know we have to reprimand you."

"Yes, Kenton, I know. Misuse of my ship, blah blah blah."

"It's a bit more serious than 'blah blah blah' Miranda."

"Well, take it away from me if you must. I'm prepared for it. I know I was in the wrong. But my crew agreed to take part in it. I didn't force anyone to go along with my husband's scheme."

"That as it may be. You've put not only your crew, but all of Zion at risk."

"Isn't the council putting Zion at risk by sanctioning Chris's plan?"

"Yes. And the council also has the authority to take that risk. You, as a captain, do not."

"So where do I stand, Kenton? Have I been relieved of duty?"

"Regretfully, yes. You have been demoted to 1st mate on the Osiris. Marco will take over as captain when the new patrol rotation begins in a fortnight. I'm sorry, Miranda, I really am. Our laws are strict for a reason. Being the last free humans in the universe leaves us on pretty shaky ground. Each of us has to do our part to keep each other alive."

"Sure, sure. I don't need a speech, Kenton. I get it. Now that that is settled I have another question to ask. What are you going to do about Reinette and Stephen?"

"There isn't a whole lot I can do. I can talk to them, try to make them see the error they make, but somehow I don't think that will change their position. Content yourself in the knowledge that they are part of a very small minority among Zion. Most of Zion, myself included, regard Christopher with a sense of quiet awe."

"To be honest, Ken, that's almost as bad as the bigotry."

--

Late that night (or perhaps early the next morning would be a better description), Christopher sat at his table watching Miranda sleep. Light from the candle he had burning played softly on her face, making her skin seem to glow. He felt the familiar rush of emotion that he always felt when he watched her.

Miranda stirred under his gaze and woke slowly, her arms searching for him and finding only an empty space where he should be. Her eyes flew open and she sat up quickly.

"I'm here, love," he called to her.

"Christ, Chris, don't scare me like that!"

Miranda rose from the bed and came to sit on Christopher's lap. He held her close, his head resting on her chest. He listened to her breathe for a few minutes before he felt her soft hands pull his chin up. She looked into his eyes for a moment.

"What is it?" she asked. "What's wrong?"

Christopher sighed.

"It's nothing, Randa. I mean, it's not that I was surprised by the reaction in council today. It's just…I mean Reinette…I had no idea…"

Miranda held her hand to his lips.

"Hush. I wondered how you would take that. Look, Reinette might have been elected to the council, and she might have the captain of the flagship of the fleet in her corner, but that doesn't mean she isn't a stuck up bitch."

Christopher laughed quietly.

"Don't you waste any brain cells on her, Chris. You're just as much of a human being as she is. Hell, you're more of a human than she is. You have a heart."

Christopher put his head back on Miranda's chest for a moment, hugging her as tightly as he could.

"How do you always know exactly what to say to make me feel better?" he whispered.

"I wouldn't be much of a wife if I didn't," she replied.

Christopher raised his head again to look deeply into her eyes. He kissed her, lightly at first, and then more deeply as his need for her washed over him. He twisted his fingers in her hair, need turning to passion as she pressed herself against him. He stood, lifting her in his arms, their embrace never breaking. He laid her down gently in their bed, climbing in beside her and allowing his hands to roam over her. She returned his touch, seeming to need him as much as he needed her. He pulled back for a moment, looking again into her bright blue eyes.

"I love you," he whispered.

"Love you too," she replied.


	8. Comfort Food

Disclaimer: The Wachowski Brothers, Warner Brothers, Joel Silver, and any number of other people own the rights to The Matrix and any and all related characters/content. Not me.

I know, I know...super short chapter. Sorry.

* * *

Seraph stood in the doorway to the Oracle's kitchen. She was baking again. The smell of oatmeal cookies permeated the air in the apartment. Behind Seraph, sitting in the living room of the apartment, ten children were gathered. They were playing games with one another, trying not to be nervous. The Oracle smiled at Seraph.

"The smell of good home cooking always sets the soul at ease. These kids have already been through a lot, so I thought oatmeal would be the most calming scent to waft around."

Seraph allowed a smile to play briefly upon his lips.

"Christopher will be returning, Oracle," Seraph said, his soft voice a stark contrast to the ever increasing volume of the children's shouts from the other room. The Oracle nodded as she rose and moved her chair from the table over to the oven.

"I think ten's enough to start off with, don't you Seraph?"

Seraph nodded once, as was his custom. The Oracle gazed into the oven, watching over her last batch of cookies.

"Of course," she said, after a moment of thought, "he won't take them all. He'll have to pick one. His choice is going to be important, Seraph, so make sure you're paying close attention. The child he chooses will be the man or woman who will find the Architect's 'One'. We have to be ready, and we have to be patient."

A far away look came into the Oracle's face, and her voice took on a dreamlike quality as she looked down the code eventualities: a million different paths and a million different futures spread out before her.

"I figure it's going to be five…maybe six iterations before something makes a difference. That's a hell of a lot of death, Seraph…"

She trailed off as Seraph approached her, laying a hand on her shoulder. She grasped his wrist for a moment before drying her eyes on a tea towel.

"Eventually," she said, "all that death will mean something. Eventually Neo will come and the game will change. We just have to play our roles out and wait for the change to come."


	9. Jacked In

Disclaimer: The Wachowski Brothers, Warner Brothers, Joel Silver, and any number of other people own the rights to The Matrix and any and all related characters/content. Not me.

Not as short as chapter 8...but still relatively short. Sorry again.

* * *

Two weeks after the council meeting, Marco quietly assumed command of the Osiris. Unknown to Kenton, Marco was captain in name only. He still consulted Miranda before he made a move.

Christopher had spent these two weeks preparing his trace program. In a burst of creativity, he decided to manifest the program as a pill to be swallowed in the Matrix. He remembered the Oracle's simple program: "Choose" it said and offered a button with a blue pill and a button with a red pill. Building on this, he created two pills to represent two programs.

The blue pill was a heavy sedative, the red his trace program. If the subject took the blue pill, they would instantly fall asleep. When they woke they would be in their own bed, still connected to the Matrix, and they would not remember a thing about Christopher or the Matrix. If the subject took the red pill, the trace would find the subject's pod and temporarily disable any machine obstacles standing in the way of freeing the person. Meanwhile, another program contained in the red pill would shock the subject's mind until it woke up. The shock would release just enough adrenalin into the subject's system to allow them to break through the membrane of the pod. The trace program would then communicate to the ship where that subject could be found. The pod would expel the subject into the sewer system and the ship would pick him or her up.

The only problem was Christopher had to be in the Matrix in order to give the pill. Up until now he hadn't needed to be connected to the Matrix. He just threw out the command for the trace and it ran. Moving from just testing the program into actually using the program on a living human required a more hands-on approach.

He still had all the ports on his body from when he had been in the pod, including the head port. He had also created a working probe that would allow him to connect himself to the Matrix as if he were still in the pod (he called it "jacking in"). Uploading and downloading himself in and out of the Matrix would be a challenge though. He had created a program he was fairly sure would do the job without killing him and taught Miranda how to control it. They hadn't tested it yet, though, and now that crunch time had arrived Christopher was becoming rather nervous about it.

"So tell me again…how's this going to work exactly?" Miranda asked.

"Well…in theory what will happen is you'll push the probe through my skull port and run the program. That should upload my mind directly into the Matrix like it does with the pod people. Then, I'll be free to move around the Matrix. The upload program will put a red pill and a blue pill into my pocket. Then, I just have to find someone to rescue, give them the pill, and that's it."

"And how will you escape?"

"Well, right now the upload is limited. It will only last for half an hour. After that, you'll have to run the download program or else my mind will get lost in the Matrix's code. That will put me back into my own head and disable the probe. Then you'll have to pull the probe out of my head and…in theory…I should wake up."

"In theory…"

"Yeah…"

Miranda pushed herself away from the computer console and turned to look at him. He was reclined in what resembled a dentist's chair from old Earth with a hole cut out of the headrest. He watched as a range of emotions ran across her face: amusement, fear, anger, annoyance, frustration. She knew only too well how horribly wrong this could go. Christopher could become just another part of the Matrix, like he had been before. He could die horrifically. He could lose his mind to madness.

Christopher got out of the chair and took Miranda into his arms.

"I know it's kind of scary to think about," he whispered, "but who else do you know with a great big hole in the back of his head?"

Miranda laughed despite herself.

"I'm sorry," she replied, "I'm just selfish. I don't want to give you up just yet."

"I know. You won't have to, trust me."

He kissed her briefly and resumed his chair. Miranda stood next to him.

"Ready?" she asked.

"As I'll ever be," he replied. "I love you."

Miranda's throat tightened.

"Love you too."

"Run it."

Miranda plunged the probe into his skull port and entered the command to launch the upload. Christopher's face froze in a silent scream for a moment, and then relaxed. Miranda set a timer for 30 minutes, started it, and then went to stand next to Christopher


	10. Martin

Disclaimer: The Wachowski Brothers, Warner Brothers, Joel Silver, and any number of other people own the rights to The Matrix and any and all related characters/content. Not me.

* * *

Christopher opened his eyes slowly. He knew he was successful because he could feel the sun warming him. He looked down at himself. He was wearing what he had been wearing the night he had freed himself from the Matrix. He laughed as he ran his fingers over the material of his clothes and through his hair. The hair on his head was long and unkempt, like it had been during his Matrix-life. _This must be my mind compensating or something_, he thought, _like a residual self-image_.

Christopher slipped a hand into his pocket. The pills were there, just as he had programmed them to be. He laughed again, looking up and down the block he was standing on. He realized it was the block that the Oracle lived on. Thinking of her brought him back to reality. He checked his wrist and found a convenient watch there, telling him he had twenty-eight minutes left. He took off running toward the Oracle's building.

Christopher took the steps up to her apartment two at a time and skidded to a halt outside her door. Seraph was standing in the doorway.

"Come in, Christopher," Seraph said. "The Oracle is expecting you."

Christopher entered slowly, put off his guard by Seraph's presence. He'd never met Seraph before. As he walked through to the kitchen, he noticed the children in the living room: another disconcerting sight. Seraph followed close behind him, almost herding him into the kitchen.

The woman Christopher saw was not at all who he was expecting.

"Who the hell are you?" he cried.

"Why Christopher, how nice to see you!" she replied. "Don't be fooled by this face, kiddo. I'm still the same woman…just look a little older."

"And a little blacker. And a little shorter. And a little…"

"Ok that's enough of that!" The Oracle laughed.

"We both know you don't have enough time to ask me all about my transformation, so let's make this quick. You came looking for a mind to free. I happen to have ten hopefuls in my living room. You're going to ask how I knew you were coming, but you already know the answer to that. You're also going to ask why children. Well, Chris, a child's mind will accept the truth a hell of a lot easier than an adult's will. I figure you start on the kids and then work your way up. I know you can only take one. I suggest you head on into the living room and make your choice."

Christopher stood dumbfounded for a moment. He heard his watch beep and glanced down. Fifteen minutes to go.

"I'll be back," he said to the Oracle. "We have unfinished business."

"Yes, we certainly do. Now get going."

Christopher flew into the living room. Ten hopeful faces looked at him. He didn't begin to know how he was going to make this decision.

One of the children had been playing with what appeared to be a bent spoon. He was older than the rest…perhaps thirteen where the rest were ten or eleven. He looked Christopher in the face for a moment, then blushed and looked away.

"What's your name, kid?" Christopher asked.

"Martin," the child replied.

"Do you know why you're here, Martin?"

"Yeah. The Oracle explained to all of us."

"Ok, I'm going to ask you a question. Do you have weird dreams?"

"Yeah. All the time."

"Do you want to know what your dreams mean? Even if you can't see your mom or dad anymore, or any of your friends?"

Martin looked back into Christopher's eyes.

"Yeah," he said softly.

Christopher took the pills from his pocket, glancing at his watch. Ten minutes…

"Ok, we don't have a lot of time. If you're really sure about that, then take the red pill in my hand. If you're not sure, take the blue pill. If you take the red pill, I have to be honest, it's going to be hard. If you take the blue pill, you'll go home and you won't remember any of this."

Martin hesitated for a moment, and then took the red pill from Christopher. He put it in his mouth, and Seraph handed him a glass of water to sip.

"Ok, Martin, listen carefully. In about a minute some scary things are going to happen to you. You're going to wake up and be surrounded by some pink goo. Don't panic, ok? There's going to be a rubbery covering on you. You need to rip through that. There's also going to be a tube down your throat. You're going to have to pull that out after you rip through the rubbery stuff, ok? Do you think you can do that for me?"

Martin nodded, fear behind his eyes. He was putting on a brave face, trying to prove to Christopher that he was worthy.

"Ok. After you take out the tube, you're going to fall. Don't be afraid."

Martin's body began to jump and shift, as if he were on a television with bad reception. Panic seeped into the boy's eyes as he looked pleadingly at Christopher.

"Listen to me, Martin! Don't be afraid! I'm coming for you, ok? You won't be alone for long!"

With this, Martin vanished before Christopher's eyes. He glanced at his watch again. Nine minutes. He walked back into the kitchen.

"Who did you pick?" she asked.

"Kid named Martin."

"I wondered if you'd pick him. He's about the age you were when you started getting into computers. He's going to be an asset to you. He knows more about computers than you did at his age. I have to say, good choice.

"Now. You only have a few minutes left so let me tell you a few things you need to know. The creator program has changed a few things in the Matrix…"

The Oracle's words were cut short by the sound of a door being kicked in. Christopher spun around and saw three men in black suits saunter casually through the doorway. Seraph stood in front of the children, who were screaming in terror. Christopher stared at the men as they advanced on him.

"Dammit, Chris, RUN!"

The Oracle's words cut through Christopher's reverie and he spun to face her.

"Where to?!"

"The window!"

Christopher ran to the window and glanced out of it. He heard the men running to intercept him as he stared briefly at the sheer five story drop. Before he thought about what he was doing, he leapt out the window. He felt one of the men grapple with his ankle, but was able to shake him off.

He seemed to fall in slow motion. He found it easy to flip his body around to land on his feet. When he landed, the concrete beneath him seemed to billow out, rippling in concentric circles from his feet. He looked up in time to see one of the men leaping out the window behind him. At that moment, his watch beeped. As the man in black closed in on him, the scene suddenly dissolved into blackness.

--

"Chris?"

Miranda's voice, strained with worry, floated through Christopher's brain. He heard a metallic click and felt the intensely odd sensation of the probe being pulled from his head. His eyes fluttered open.

"Oh thank God, Chris, you're all right!"

Miranda threw herself over Christopher, hugging him fiercely.

"Told ya I'd be ok," Christopher said, hugging her back and laughing. "Did you find the kid?"

"Yeah. The ship received his signature about five minutes before I pulled you out. We're en route now. What happened, Chris? At one point, right before your time was up, there was a weird blip in your brainwaves."

"I'm not quite sure. I mean, the plan itself went off without a hitch. The kid took the pill, about a minute later he phased out of the Matrix, it all went like clockwork. But then those men…those agents or whatever they are…they showed up, gunning for me. So I jumped out the window…and the weirdest thing happened. For a minute, I swear instead of the landscape I saw the coding of the Matrix program. And I changed part of it, so that I landed on my feet."

"You…saw the code?"

"Yeah. I swear I did. And then one of the agents jumped out the window after me. You pulled me out just in time, Randa."

Just then, the intercom crackled to life.

"We're coming up on the pod person now, Miranda. You might want to get up here."

Christopher grabbed her hand as she turned to go.

"I'm coming too. I told Martin I was coming for him."


	11. Webs

Disclaimer: The Wachowski Brothers, Warner Brothers, Joel Silver, and any number of other people own the rights to The Matrix and any and all related characters/content. Not me.

* * *

Reinette and Stephen sat in their living quarters, discussing their plans.

"Something had to be done about him, Stephen. He's out there right now, scooping up another battery to add to his arsenal."

"Well you're on the council. Can't you get Kenton to stop it?"

"You know I've tried! Kenton seems to think since three captains are on _its_ side, _it_ has the right to pollute us with the batteries."

"I haven't had any luck with the captains either. Of course Miranda won't be of any use to us. She loves her _pet_. Leah has Samuel wrapped around her finger. He'll do whatever she tells him to do."

"What about Marlin?"

"Marlin's not on our side. She might think Christopher is in the wrong, but she doesn't see him for the battery he is. She actually likes him!"

"Well I know Michael is on our side. And I think with a little persuasion I can get Gregory to see our point of view. But Kenton will not be moved."

"What about Margot and the twins?"

"Not a chance. They're all sympathetic to Leah, which means they're on the battery's side."

"What's to be done, then? _Diplomacy_ is obviously failing us."

"This has to be stopped before it goes any further. The rabble already thinks the battery is their God. Saintly, godlike Abe. It makes me sick. And now, _now_ the battery's out there bringing more batteries to Zion. The battery has to die, Stephen. Quickly."

"Not too quickly, love. We'll need to think this through. We need a plan before we go murdering the _chosen one_."

--

Christopher and Miranda stood next to Martin's bed as Andy tended to him.

"Martin? It's Christopher, can you hear me?"

"He's out cold. He saw you before he passed out though. Andy thinks he knows he's safe."

"That's good, anyway. God, Randa, he looks so much younger here than he did in the Matrix."

"Yeah, he is pretty young. That's good though, right? I mean…he'll heal faster. And like the Oracle told you, he'll accept the truth easier than an adult."

"I guess you're right. He just looks so…fragile."

Miranda put an arm around Christopher's waist.

"I know, Chris. But he'll be ok. He's got you and me, and Andy and Marco. We'll be his family now and we'll keep him safe."

"That's right," Andy said. "He'll be just fine, Abe, you wait and see."

Christopher's head snapped up and he looked at Andy, dumbfounded.

"Since when do you call me Abe, Andy?"

"You saw the code, man. You could see computer code. You freed yourself from the Matrix. And you saved this kid. Nothing for nothing, Abe, but I think that deserves some respect."

Christopher saw the awe in Andy's eyes. Sadness washed over him as he saw his friend turning before his eyes into an acolyte.

"Aw, Andy…Andy, I'm still just Chris. Sure, some weird shit has happened to me…but I'm still just me."

Andy shook his head.

"Sorry, man. There's something special about you, and I can't help but believe."

--

The Architect watched Christopher freeing Martin for the nth time on his monitors. Once again, his agents had failed to prevent an escape. He knew escapes were inevitable now, but he had at least hoped the agents would be a deterrent.

And of course, _she_ had helped. _She_ was becoming insufferable. The Architect knew he couldn't destroy her because of her tame program who exploited "back doors." But perhaps…perhaps there was a way to put an obstacle in her path.

The Architect began to write a new agent program. _An upgrade_, he thought. Since the current program seemed to be…ineffectual…he would simply change the program.

He allowed himself to smile. The new agent programs would be difficult to circumvent. He sat back in his chair and clicked off the monitors. He was interested to see how she would deal with this new variable in the equation.

End

To be Continued

* * *

Postscript: Yay for more cliffhangers! Thanks for reading and we'll see you in part three!!


End file.
